Background: Duodenal gastrointestinal stromal tumors (GISTs) are rare and their clinicopathological features have not been completely described. In this retrospective study, we examined the characteristics and long-term outcomes of patients who underwent surgical treatment for duodenal GISTs. Methods: We examined patients surgically treated for duodenal GISTs from 1999 to 2016 at the China National Cancer Center. We analyzed patient characteristics, treatments, histological examinations, and survival outcomes. Results: The 52 surgeries performed included 14 pancreaticoduodenectomies (26.9%), 37 limited resections (71.2%), and one palliative bypass procedure (1.9%). No surgery-related death occurred. The complication rate in patients who underwent pancreaticoduodenectomy was slightly higher than that in patients who underwent limited resection. The 5-year overall survival and progression-free survival rates for patients with duodenal adenocarcinoma were 89.1 and 72.9%, respectively. The overall survival and progression-free survival rates were not significantly related to surgical methods. Large tumor size and high mitotic rate were associated with poor overall survival outcomes. However, no independent factor was associated with prognosis, which may be due to the small sample size. Conclusion: The prognosis of duodenal gastrointestinal stromal tumors was good. Limited resection seems to be oncologically feasible, with outcomes being less worse than those of pancreaticoduodenectomy.